OpenRaiser/Intern-Atlas huggingface dataset:
Combinatorial Reasoning: Selecting Reasons in Generative AI Pipelines via Combinatorial Optimization
Venue: arXiv cs.AI 2024
Year: 2024

Recent Large Language Models (LLMs) have demonstrated impressive capabilities at tasks that require human intelligence and are a significant step towards human-like artificial intelligence (AI). Yet the performance of LLMs at reasoning tasks have been subpar and the reasoning capability of LLMs is a matter of significant debate. While it has been shown that the choice of the prompting technique to the LLM can alter its performance on a multitude of tasks, including reasoning, the best performing techniques require human-made prompts with the knowledge of the tasks at hand. We introduce a framework for what we call Combinatorial Reasoning (CR), a fully-automated prompting method, where reasons are sampled from an LLM pipeline and mapped into a Quadratic Unconstrained Binary Optimization (QUBO) problem. The framework investigates whether QUBO solutions can be profitably used to select a useful subset of the reasons to construct a Chain-of-Thought style prompt. We explore the acceleration of CR with specialized solvers. We also investigate the performance of simpler zero-shot strategies such as linear majority rule or random selection of reasons. Our preliminary study indicates that coupling a combinatorial solver to generative AI pipelines is an interesting avenue for AI reasoning and elucidates design principles for future CR methods.
Multiple Kronecker RLS fusion-based link propagation for drug-side effect prediction
Venue: arXiv cs.LG 2024
Year: 2024

Drug-side effect prediction has become an essential area of research in the field of pharmacology. As the use of medications continues to rise, so does the importance of understanding and mitigating the potential risks associated with them. At present, researchers have turned to data-driven methods to predict drug-side effects. Drug-side effect prediction is a link prediction problem, and the related data can be described from various perspectives. To process these kinds of data, a multi-view method, called Multiple Kronecker RLS fusion-based link propagation (MKronRLSF-LP), is proposed. MKronRLSF-LP extends the Kron-RLS by finding the consensus partitions and multiple graph Laplacian constraints in the multi-view setting. Both of these multi-view settings contribute to a higher quality result. Extensive experiments have been conducted on drug-side effect datasets, and our empirical results provide evidence that our approach is effective and robust.
Efficient Long-distance Latent Relation-aware Graph Neural Network for Multi-modal Emotion Recognition in Conversations
Venue: arXiv cs.LG 2024
Year: 2024

The task of multi-modal emotion recognition in conversation (MERC) aims to analyze the genuine emotional state of each utterance based on the multi-modal information in the conversation, which is crucial for conversation understanding. Existing methods focus on using graph neural networks (GNN) to model conversational relationships and capture contextual latent semantic relationships. However, due to the complexity of GNN, existing methods cannot efficiently capture the potential dependencies between long-distance utterances, which limits the performance of MERC. In this paper, we propose an Efficient Long-distance Latent Relation-aware Graph Neural Network (ELR-GNN) for multi-modal emotion recognition in conversations. Specifically, we first use pre-extracted text, video and audio features as input to Bi-LSTM to capture contextual semantic information and obtain low-level utterance features. Then, we use low-level utterance features to construct a conversational emotion interaction graph. To efficiently capture the potential dependencies between long-distance utterances, we use the dilated generalized forward push algorithm to precompute the emotional propagation between global utterances and design an emotional relation-aware operator to capture the potential semantic associations between different utterances. Furthermore, we combine early fusion and adaptive late fusion mechanisms to fuse latent dependency information between speaker relationship information and context. Finally, we obtain high-level discourse features and feed them into MLP for emotion prediction. Extensive experimental results show that ELR-GNN achieves state-of-the-art performance on the benchmark datasets IEMOCAP and MELD, with running times reduced by 52\% and 35\%, respectively.
The Qiyas Benchmark: Measuring ChatGPT Mathematical and Language Understanding in Arabic
Venue: arXiv cs.CL 2024
Year: 2024

Despite the growing importance of Arabic as a global language, there is a notable lack of language models pre-trained exclusively on Arabic data. This shortage has led to limited benchmarks available for assessing language model performance in Arabic. To address this gap, we introduce two novel benchmarks designed to evaluate models' mathematical reasoning and language understanding abilities in Arabic. These benchmarks are derived from a General Aptitude Test (GAT) called Qiyas exam, a standardized test widely used for university admissions in Saudi Arabia. For validation purposes, we assess the performance of ChatGPT-3.5-trubo and ChatGPT-4 on our benchmarks. Our findings reveal that these benchmarks pose a significant challenge, with ChatGPT-4 achieving an overall average accuracy of 64%, while ChatGPT-3.5-trubo achieved an overall accuracy of 49% across the various question types in the Qiyas benchmark. We believe the release of these benchmarks will pave the way for enhancing the mathematical reasoning and language understanding capabilities of future models tailored for the low-resource Arabic language.
Localizing Anomalies via Multiscale Score Matching Analysis
Venue: arXiv cs.CV 2024
Year: 2024

Anomaly detection and localization in medical imaging remain critical challenges in healthcare. This paper introduces Spatial-MSMA (Multiscale Score Matching Analysis), a novel unsupervised method for anomaly localization in volumetric brain MRIs. Building upon the MSMA framework, our approach incorporates spatial information and conditional likelihoods to enhance anomaly detection capabilities. We employ a flexible normalizing flow model conditioned on patch positions and global image features to estimate patch-wise anomaly scores. The method is evaluated on a dataset of 1,650 T1- and T2-weighted brain MRIs from typically developing children, with simulated lesions added to the test set. Spatial-MSMA significantly outperforms existing methods, including reconstruction-based, generative-based, and interpretation-based approaches, in lesion detection and segmentation tasks. Our model achieves superior performance in both distance-based metrics (99th percentile Hausdorff Distance: $7.05 \pm 0.61$, Mean Surface Distance: $2.10 \pm 0.43$) and component-wise metrics (True Positive Rate: $0.83 \pm 0.01$, Positive Predictive Value: $0.96 \pm 0.01$). These results demonstrate Spatial-MSMA's potential for accurate and interpretable anomaly localization in medical imaging, with implications for improved diagnosis and treatment planning in clinical settings. Our code is available at~\url{https://github.com/ahsanMah/sade/}.
PathGen-1.6M: 1.6 Million Pathology Image-text Pairs Generation through Multi-agent Collaboration
Venue: arXiv cs.CV 2024
Year: 2024

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.
A flexured-gimbal 3-axis force-torque sensor reveals minimal cross-axis coupling in an insect-sized flapping-wing robot
Venue: arXiv cs.RO 2024
Year: 2024

The mechanical complexity of flapping wings, their unsteady aerodynamic flow, and challenge of making measurements at the scale of a sub-gram flapping-wing flying insect robot (FIR) make its behavior hard to predict. Knowing the precise mapping from voltage input to torque output, however, can be used to improve their mechanical and flight controller design. To address this challenge, we created a sensitive force-torque sensor based on a flexured gimbal that only requires a standard motion capture system or accelerometer for readout. Our device precisely and accurately measures pitch and roll torques simultaneously, as well as thrust, on a tethered flapping-wing FIR in response to changing voltage input signals. With it, we were able to measure cross-axis coupling of both torque and thrust input commands on a 180 mg FIR, the UW Robofly. We validated these measurements using free-flight experiments. Our results showed that roll and pitch have maximum cross-axis coupling errors of 8.58% and 17.24%, respectively, relative to the range of torque that is possible. Similarly, varying the pitch and roll commands resulted in up to a 5.78% deviation from the commanded thrust, across the entire commanded torque range. Our system, the first to measure two torque axes simultaneously, shows that torque commands have a negligible cross-axis coupling on both torque and thrust.
SemUV: Deep Learning based semantic manipulation over UV texture map of virtual human heads
Venue: arXiv cs.CV 2024
Year: 2024

Designing and manipulating virtual human heads is essential across various applications, including AR, VR, gaming, human-computer interaction and VFX. Traditional graphic-based approaches require manual effort and resources to achieve accurate representation of human heads. While modern deep learning techniques can generate and edit highly photorealistic images of faces, their focus remains predominantly on 2D facial images. This limitation makes them less suitable for 3D applications. Recognizing the vital role of editing within the UV texture space as a key component in the 3D graphics pipeline, our work focuses on this aspect to benefit graphic designers by providing enhanced control and precision in appearance manipulation. Research on existing methods within the UV texture space is limited, complex, and poses challenges. In this paper, we introduce SemUV: a simple and effective approach using the FFHQ-UV dataset for semantic manipulation directly within the UV texture space. We train a StyleGAN model on the publicly available FFHQ-UV dataset, and subsequently train a boundary for interpolation and semantic feature manipulation. Through experiments comparing our method with 2D manipulation technique, we demonstrate its superior ability to preserve identity while effectively modifying semantic features such as age, gender, and facial hair. Our approach is simple, agnostic to other 3D components such as structure, lighting, and rendering, and also enables seamless integration into standard 3D graphics pipelines without demanding extensive domain expertise, time, or resources.
Methodology to Deploy CNN-Based Computer Vision Models on Immersive Wearable Devices
Venue: arXiv cs.CV 2024
Year: 2024

Convolutional Neural Network (CNN) models often lack the ability to incorporate human input, which can be addressed by Augmented Reality (AR) headsets. However, current AR headsets face limitations in processing power, which has prevented researchers from performing real-time, complex image recognition tasks using CNNs in AR headsets. This paper presents a method to deploy CNN models on AR headsets by training them on computers and transferring the optimized weight matrices to the headset. The approach transforms the image data and CNN layers into a one-dimensional format suitable for the AR platform. We demonstrate this method by training the LeNet-5 CNN model on the MNIST dataset using PyTorch and deploying it on a HoloLens AR headset. The results show that the model maintains an accuracy of approximately 98%, similar to its performance on a computer. This integration of CNN and AR enables real-time image processing on AR headsets, allowing for the incorporation of human input into AI models.
The Even-Path Problem in Directed Single-Crossing-Minor-Free Graphs
Venue: arXiv cs.DS 2024
Year: 2024

Finding a simple path of even length between two designated vertices in a directed graph is a fundamental NP-complete problem known as the EvenPath problem. Nedev proved in 1999, that for directed planar graphs, the problem can be solved in polynomial time. More than two decades since then, we make the first progress in extending the tractable classes of graphs for this problem. We give a polynomial time algorithm to solve the EvenPath problem for classes of H-minor-free directed graphs,1 where H is a single-crossing graph. We make two new technical contributions along the way, that might be of independent interest. The first, and perhaps our main, contribution is the construction of small, planar, parity-mimicking networks. These are graphs that mimic parities of all possible paths between a designated set of terminals of the original graph. Finding vertex disjoint paths between given source-destination pairs of vertices is another fundamental problem, known to be NP-complete in directed graphs, though known to be tractable in planar directed graphs. We encounter a natural variant of this problem, that of finding disjoint paths between given pairs of vertices, but with constraints on parity of the total length of paths. The other significant contribution of our paper is to give a polynomial time algorithm for the 3-disjoint paths with total parity problem, in directed planar graphs with some restrictions (and also in directed graphs of bounded treewidth).
EHRmonize: A Framework for Medical Concept Abstraction from Electronic Health Records using Large Language Models
Venue: arXiv cs.CL 2024
Year: 2024

Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize, a framework leveraging LLMs to abstract medical concepts from EHR data. Our study uses medication data from two real-world EHR databases to evaluate five LLMs on two free-text extraction and six binary classification tasks across various prompting strategies. GPT-4o's with 10-shot prompting achieved the highest performance in all tasks, accompanied by Claude-3.5-Sonnet in a subset of tasks. GPT-4o achieved an accuracy of 97% in identifying generic route names, 82% for generic drug names, and 100% in performing binary classification of antibiotics. While EHRmonize significantly enhances efficiency, reducing annotation time by an estimated 60%, we emphasize that clinician oversight remains essential. Our framework, available as a Python package, offers a promising tool to assist clinicians in EHR data abstraction, potentially accelerating healthcare research and improving data harmonization processes.
SBOM.EXE: Countering Dynamic Code Injection based on Software Bill of Materials in Java
Venue: arXiv cs.CR 2024
Year: 2024

Software supply chain attacks have become a significant threat as software development increasingly relies on contributions from multiple, often unverified sources. The code from unverified sources does not pose a threat until it is executed. Log4Shell is a recent example of a supply chain attack that processed a malicious input at runtime, leading to remote code execution. It exploited the dynamic class loading facilities of Java to compromise the runtime integrity of the application. Traditional safeguards can mitigate supply chain attacks at build time, but they have limitations in mitigating runtime threats posed by dynamically loaded malicious classes. This calls for a system that can detect these malicious classes and prevent their execution at runtime. This paper introduces SBOM.EXE, a proactive system designed to safeguard Java applications against such threats. SBOM.EXE constructs a comprehensive allowlist of permissible classes based on the complete software supply chain of the application. This allowlist is enforced at runtime, blocking any unrecognized or tampered classes from executing. We assess SBOM.EXE's effectiveness by mitigating 3 critical CVEs based on the above threat. We run our tool with 3 open-source Java applications and report that our tool is compatible with real-world applications with minimal performance overhead. Our findings demonstrate that SBOM.EXE can effectively maintain runtime integrity with minimal performance impact, offering a novel approach to fortifying Java applications against dynamic classloading attacks.
Leveraging Fixed-Parameter Tractability for Robot Inspection Planning
Venue: arXiv cs.RO 2024
Year: 2024

Autonomous robotic inspection, where a robot moves through its environment and inspects points of interest, has applications in industrial settings, structural health monitoring, and medicine. Planning the paths for a robot to safely and efficiently perform such an inspection is an extremely difficult algorithmic challenge. In this work we consider an abstraction of the inspection planning problem which we term Graph Inspection. We give two exact algorithms for this problem, using dynamic programming and integer linear programming. We analyze the performance of these methods, and present multiple approaches to achieve scalability. We demonstrate significant improvement both in path weight and inspection coverage over a state-of-the-art approach on two robotics tasks in simulation, a bridge inspection task by a UAV and a surgical inspection task using a medical robot.
External Model Motivated Agents: Reinforcement Learning for Enhanced Environment Sampling
Venue: arXiv cs.AI 2024
Year: 2024

Unlike reinforcement learning (RL) agents, humans remain capable multitaskers in changing environments. In spite of only experiencing the world through their own observations and interactions, people know how to balance focusing on tasks with learning about how changes may affect their understanding of the world. This is possible by choosing to solve tasks in ways that are interesting and generally informative beyond just the current task. Motivated by this, we propose an agent influence framework for RL agents to improve the adaptation efficiency of external models in changing environments without any changes to the agent's rewards. Our formulation is composed of two self-contained modules: interest fields and behavior shaping via interest fields. We implement an uncertainty-based interest field algorithm as well as a skill-sampling-based behavior-shaping algorithm to use in testing this framework. Our results show that our method outperforms the baselines in terms of external model adaptation on metrics that measure both efficiency and performance.
PerAct2: Benchmarking and Learning for Robotic Bimanual Manipulation Tasks
Venue: arXiv cs.RO 2024
Year: 2024

Bimanual manipulation is challenging due to precise spatial and temporal coordination required between two arms. While there exist several real-world bimanual systems, there is a lack of simulated benchmarks with a large task diversity for systematically studying bimanual capabilities across a wide range of tabletop tasks. This paper addresses the gap by extending RLBench to bimanual manipulation. We open-source our code and benchmark comprising 13 new tasks with 23 unique task variations, each requiring a high degree of coordination and adaptability. To kickstart the benchmark, we extended several state-of-the art methods to bimanual manipulation and also present a language-conditioned behavioral cloning agent -- PerAct2, which enables the learning and execution of bimanual 6-DoF manipulation tasks. Our novel network architecture efficiently integrates language processing with action prediction, allowing robots to understand and perform complex bimanual tasks in response to user-specified goals. Project website with code is available at: http://bimanual.github.io
On Line-Separable Weighted Unit-Disk Coverage and Related Problems
Venue: arXiv cs.CG 2024
Year: 2024

Given a set $P$ of $n$ points and a set $S$ of $n$ weighted disks in the plane, the disk coverage problem is to compute a subset of disks of smallest total weight such that the union of the disks in the subset covers all points of $P$. The problem is NP-hard. In this paper, we consider a line-separable unit-disk version of the problem where all disks have the same radius and their centers are separated from the points of $P$ by a line $\ell$. We present an $O(n^{3/2}\log^2 n)$ time algorithm for the problem. This improves the previously best work of $O(n^2\log n)$ time. Our result leads to an algorithm of $O(n^{{7}/{2}}\log^2 n)$ time for the halfplane coverage problem (i.e., using $n$ weighted halfplanes to cover $n$ points), an improvement over the previous $O(n^4\log n)$ time solution. If all halfplanes are lower ones, our algorithm runs in $O(n^{{3}/{2}}\log^2 n)$ time, while the previous best algorithm takes $O(n^2\log n)$ time. Using duality, the hitting set problems under the same settings can be solved with similar time complexities.
Unicorns Do Not Exist: Employing and Appreciating Community Managers in Open Source
Venue: arXiv cs.SE 2024
Year: 2024

Open-source software is released under an open-source licence, which means the software can be shared, adapted, and reshared without prejudice. In the context of open-source software, community managers manage the communities that contribute to the development and upkeep of open-source tools. Despite playing a crucial role in maintaining open-source software, community managers are often overlooked. In this paper we look at why this happens and the troubling future we are heading towards if this trend continues. Namely if community managers are driven to focus on corporate needs and become conflicted with the communities they are meant to be managing. We suggest methods to overcome this by stressing the need for the specialisation of roles and by advocating for transparent metrics that highlight the real work of the community manager. Following these guidelines can allow this vital role to be treated with the transparency and respect that it deserves, alongside more traditional roles including software developers and engineers.